2006

VOLUME 1
NUMBER 2

TM

Molecular Self-Assembly
Introduction to
Molecular Self-Assembly

Self-Assembled
Monolayers (SAMs)

Microdisplacement
Printing

Self-Assembly in
Flexible Electronics

High Affinity Polyvalent

NanotethersTM

Biotechnology
Biosensor Program

Protocol for SAMs

Preparation

Spontaneously assemble a computer

chip....Fact or Fiction?

sigma-aldrich.com
 

Introduction
Welcome to the second issue of Material MattersTM. This thematic issue focuses on self- TM

assembly and its application for the production of nanodevices. The ability to organize
matter using self-assembled monolayers (SAMs) is part of the broader approach of
Molecular Self-Assembly as introduced by Dr. Jasty of Sigma-Aldrich Materials Science. Vol. 1 No. 2
Scientists from Assemblon discuss the importance of purity in enhancing the integrity
and kinetics of SAMs formation. The Weiss group from Penn State University illustrates
the principle of microdisplacement printing, a SAMs technique to fabricate precise, Aldrich Chemical Co., Inc.
complex patterns at the nanoscale. Prof. Bao of Stanford University surveys the Sigma-Aldrich Corporation
latest developments in the application of SAMs for the fabrication of organic thin 6000 N. Teutonia Ave.
film transistors. Borrowing a basic concept of biomolecular recognition, polyvalent Milwaukee, WI 53209, USA
interactions, the team at Sensopath Technologies engineers robust NanotethersTM as the
SAMs molecules for biosensor and other applications. We invite you to participate in
the Sigma-Aldrich Biosensor program. Finally, in keeping with the theme of a technical To Place Orders
Introduction

guide, this issue of Material Matters includes a step-by-step protocol for the preparation
of SAMs. Products that accelerate your research in the fundamental science of SAMs,
and the application of SAMs for the fabrication of nanodevices are highlighted. For
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s i g m a - a l d r i c h . c o m

What would it take to spontaneously assemble a computer chip, or for that matter any
complex structure? Starting with constituent molecules such as the one featured on
All prices are subject to change without notice.
our cover, (11-Mercaptoundecyl)tri(ethylene glycol), and with recent advances in micro-
and nanoscale science, scientists from numerous disciplines, chemistry, physics, biology,
Material Matters is a publication of Aldrich Chemical
engineering, and mathematics to name a few, have begun to investigate the self-assembly
Co., Inc. Aldrich is a member of the Sigma-Aldrich
process in hopes of learning to create, design and control self-assembling systems.
Group. © 2006 Sigma-Aldrich Co.

Introduction to Molecular
Self-Assembly
Dr. Shashi Jasty, Sigma-Aldrich Materials Science
Molecular self-assembly is the assembly of molecules without
guidance or management from an outside source. Self-
assembly can occur spontaneously in nature, for example, in
cells such as the self-assembly of the lipid bilayer membrane.
It usually results in an increase in internal organization of the
system. Many biological systems use self-assembly to assemble
various molecules and structures. Imitating these strategies
and creating novel molecules with the ability to self-assemble
into supramolecular assemblies is an important technique in
nanotechnology.
In self-assembly, the final (desired) structure is ‘encoded’ in
the shape and properties of the molecules that are used, as
compared to traditional techniques, such as lithography, where
the desired final structure must be carved out from a larger
block of matter. Self-assembly is thus referred to as a ‘bottom-
up’ manufacturing technique, as compared to lithography
being a ‘top-down’ technique.
On a molecular scale, the accurate and controlled application
of intermolecular forces can lead to new and previously
unachievable nanostructures. This is why molecular self-
assembly (MSA) is a highly topical and promising field of
research in nanotechnology today. With many complex
examples all around us in nature (ourselves included), MSA
is a widely observed phenomenon that has yet to be fully
understood. Biomolecular assemblies are sophisticated and
often hard to isolate, making systematic and progressive
analyses of their fundamental science very difficult. What in
fact are needed are simpler MSAs, the constituent molecules of
which can be readily synthesized by chemists. These molecules
would self-assemble into simpler constructs that can be easily
assessed with current experimental techniques.
Of the diverse approaches possible for Molecular Self-Assembly,
two strategies have received significant research attention
– Electrostatic Self-Assembly (or layer- by-layer assembly)
and “Self-Assembled Monolayers (SAMs). Electrostatic self-
assembly involves the alternate adsorption of anionic and
cationic electrolytes onto a suitable substrate. Typically, only
one of these is the active layer while the other enables the
composite multilayered film to be bound by electrostatic
attraction. The latter strategy of Self Assembled Monolayers
or SAMs based on constituent molecules, such as thiols and
silanes, is the theme for this second issue of Material MattersTM.
For SAMs, synthetic chemistry is used only to construct the
basic building blocks (that is, the constituent molecules), and
weaker intermolecular bonds such as Van der Waals bonds
are involved in arranging and binding the blocks together into
a structure. This weak bonding makes solution, and hence
reversible, processing of SAMs (and in general, MSAs) possible.
Thus, solution processing and manufacturing of SAMs offer
the enviable goal of mass production with the possibility of
error correction at any stage of assembly. It is well recognized
that this method could prove to be the most cost-effective
way for the semiconductor electronics industry to produce
functional nanodevices such as nanowires, nanotransistors, and
nanosensors in large numbers.
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Self-Assembled Monolayers:
Advantages of Pure Alkanethiols
Dr. Maxi Boeckl and
Dr. Daniel Graham,
Senior Scientists,
Asemblon, Inc.
Self-Assembly: From Nature to The Lab
In the 1980’s, scientists discovered that alkanethiols
spontaneously assembled on noble metals. This new area of
science opened the doors to a simple way of creating surfaces
Self-Assembly
Introduction to Molecular
of virtually any desired chemistry by placing a gold substrate
into a millimolar solution of an alkanethiol in ethanol. This
results in crystalline-like monolayers formed on the metal
surface, called self-assembled monolayers (SAMs).1
Over the years, the mechanism of the self-assembly process
has been well studied and elucidated. Researchers have found
that a typical alkanethiol monolayer forms a (√3 × √3)R30°
structure2 on gold with the thiol chains tilted approximately 30
degrees from the surface normal.3–6 The exact structure of the
monolayer depends on the chemistry of the chain.
Self-assembly forms the basis for many natural processes
including protein folding, DNA transcribing and hybridization,
and the formation of cell membranes. The process of self-
assembly in nature is governed by inter- and intra-molecular
forces that drive the molecules into a stable, low energy
state. These forces include hydrogen bonding, electrostatic
interactions, hydrophobic interactions, and van der Waals forces.
As with self-assembly in nature, there are several driving forces
for the assembly of alkanethiols onto noble metal surfaces. The
first is the affinity of sulfur for the gold surface. Researchers
O r d e r :
have found that the sulfur-gold interaction is on the order of 45
kcal/mol,3 forming a stable, semi-covalent bond; in comparison,
the C—C bond strength is ~83 kcal/mol.
1 . 8 0 0 . 3 2 5 . 3 0 1 0
The next driving force for assembly is the hydrophobic, van
der Waals interactions between the methylene carbons on
the alkane chains. For alkanethiol monolayers, this interaction
causes the thiol chains to tilt in order to maximize the
interaction between the chains and lower the overall surface
energy. A well-ordered monolayer forms from an alkane chain
of at least 10 carbons. With carbon chains of this length,
hydrophobic interactions between the chains can overcome the
molecules’ rotational degrees of freedom.6,7
Te c h n i c a l
A simple alkanethiol molecule is shown in Figure 1. (next
page) An alkanethiol can be thought of as containing 3 parts:
a sulfur binding group for attachment to a noble metal surface,
a spacer chain (typically made up of methylene groups, (CH2)n),
and a functional head group. As mentioned above, the sulfur
atom and the carbons in the methylene groups act as the main
S e r v i c e :
driving forces for assembly of the alkanethiols. The head group
then provides a platform where any desired group can be used
to produce surfaces of effectively any type of chemistry.
By simply changing the head group, a surface can be created
that is hydrophobic (methyl head group), hydrophilic (hydroxyl
1 . 8 0 0 . 2 3 1 . 8 3 2 7
or carboxyl head group), protein resistant (ethlylene glycol head
group), or allows chemical binding (NTA, azide, carboxyl, amine
head groups). This enables a researcher to custom design a
surface to serve any desired function.
 
Head
Group
Head Group
Spacer Group
Terminal
Sulfur
Group
C12 Thiol
Substrate
SH
Self-Assembled
of Pure Alkanethiols
Monolayers: Advantages
Figure 1. Schematic diagram of a thiol molecule.
The sulfur group links the molecule to the gold surface. The head group can
be designed to provide virtually any surface chemistry, binding capacity, or
property.
Self-Assembly: Purity Matters
SAMs are typically made from a 1 mM solution of the desired
alkanethiol in ethanol. Initial monolayer formation is very fast,
with monolayer coverage being achieved within seconds to
minutes. This initially formed monolayer is not well ordered
and contains many gauche defects within the chains. Over
time, the layers become more ordered and well packed.
Reported assembly times vary throughout the literature, but
typically are 12 hours to 2 days.
The formation of a well-assembled monolayer can depend on
the purity of the alkanethiol being used. The presence of even
low levels of contaminants can result in a disordered, non-
ideal monolayer. Many typical impurities in thiol compounds
are thiolated precursor molecules that were not separated
during the purification process. These precursor molecules
can either be straight chain alkanethiols that lack the head
groups of the final product, or they can be molecules used to
introduce the thiol functional group to a precursor molecule
(such as thioacetic acid). Since these compounds also contain
thiol functionalities, they can compete with the alkanethiol
of interest for available surface locations. Competitive
adsorption can be particularly problematic for alkanethiols
with complex or bulky head groups. Bulky head groups can
reduce the driving force for assembly by disrupting the close
packed arrangement of the alkane chains. With this reduced
driving force for assembly, the straight chain or small thiol
contaminants can out-compete the alkanethiol of interest on
the surface.
These effects were noticed in early alkanethiol self-assembly
research and several detailed studies were performed on the
preferential adsorption of one alkanethiol versus another.
Adsorption from a dilute solution in ethanol of a mixture of
two alkanethiols, one with a polar the other with a nonpolar
head group, showed that adsorption of the alkanethiol with
the nonpolar head group was favored.7 Bain et al. also noticed
that alkanethiols with equivalent head groups, but longer
chains adsorbed preferentially over shorter alkanethiols. 4
When one tries to intentionally obtain a mixed monolayer,
s i g m a - a l d r i c h . c o m
where two or more head groups are present at a desired ratio,
it is very difficult to predict the relative surface concentration
from the solution concentration and a calibration curve is
typically necessary.4 An example is given by Nelson et al.,
who studied mixed monolayers of biotinylated alkanethiol
mixed with either mercaptohexadecane or (1-mercapto-11-
TO ORDER: Contact your local Sigma-Aldrich office (see back cover),
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undecyl)tetra(ethylene glycol) and correlated the solution
concentration to the surface concentration using electron
spectroscopy for chemical analysis (ESCA) and Time-of-
Flight Secondary Mass Spectrometry (ToF-SIMS).8 This study
demonstrated how the surface and solution composition in
mixed monolayers can vary significantly and why a calibration
curve is necessary when engineering mixed monolayer
surfaces.
As a demonstration of the effects of thiol impurities in SAM
formation, Table 1 shows ESCA surface composition data
from a series of SAMs prepared from thiol solutions that
were purposely spiked with “impurities”. For this experiment,
solutions of (1-mercapto-11-undecyl)tetra(ethylene glycol)
(PEG4 thiol, Aldrich Prod. No. 674508) were mixed with 0%,
1% and 10% (v/v) thioacetic acid (TAA). All monolayers
were prepared from 1 mM solutions in absolute ethanol.
The percentages shown for the various thiol components are
volume percentages.
The first observation noted from Table 1 is the increase in
the atomic percentage of gold with increasing amount of
thioacetic acid in the assembly solution. The gold signal comes
from the gold substrate underlying the monolayer. This gold
signal is attenuated by the overlying monolayer film. A thinner
or more disordered overlayer causes a decrease in signal
attenuation (increase in the gold signal). This suggests that the
addition of even 1% thioacetic acid to the assembly solution
caused a marked decrease in the monolayer thickness.
Thioacetic acid is a small molecule which if inserted into the
monolayer would disrupt the local monolayer order causing
the noted decrease in the layer thickness.
Table 1. ESCA composition data from PEG4 thiol monolayers with and
without “impurities”. All data is shown in atomic percent. Two analysis
spots are shown for each sample.
Sample=
(soln percentage) C 1s O 1s S 2p Au 4f
PEG4thiol (100%) 64.5 19.1 1.3 15.1
PEG4thiol (100%) 65.3 20.9 1.2 12.6
PEG4thiol/TAA (99%/1%) 55.9 17.3 2.3 24.5
PEG4thiol/TAA (99%/1%) 56.2 17.3 2.8 23.7
PEG4thiol/TAA (90%/10%) 45.6 12 4.3 38.1
PEG4thiol/TAA (90%/10%) 46.2 13.6 4 36.2
=
PEG4 thiol = (1-mercapto-11-undecyl)tetra(ethylene glycol); Aldrich
Prod. No. 674508 TAA = thioacetic acid
Table 2 shows the data from Table 1 rescaled without the
gold signal. This allows comparison of the atomic percentages
with that expected based on the solution mixture atomic
composition. As seen in Table 2, the experimental values
compare well with the calculated values. The atomic
percentage of sulfur is typically observed to be lower than
expected due to attenuation by the overlying monolayer. This
is the case for the 100% PEG4thiol. The fact that the sulfur
data from the other two monolayers is close to the predicted
numbers, suggests that the layers are disordered (consistent
with the gold atomic percentages) or that there is a high
amount of thioacetic acid on the surface (which has a high
relative percentage of sulfur vs. the other atoms).
 US $ 

It is interesting to note that when looking at Table 2, one Self-Assembly: Unlimited Opportunities
might think that since the relative percentages of carbon and
SAMs have been used for studies and applications in many
oxygen do not change significantly from sample to sample,
areas. A few examples include surface wetting, non-fouling
that the surfaces are still pure PEG4 thiol. It is only the high
property, electrochemistry, surface passivation, protein binding,
percentage of sulfur that sets the samples apart and indicates
DNA assembly, corrosion resistance, biological arrays, cell
that an impurity is likely present.
interactions, and molecular electronics. These and other topics
Overall, this data demonstrates that even small amounts of have been summarized in previous review articles.11-13
contaminants in a solution can cause significant differences
SAMs have truly opened the doors toward direct surface
in the monolayer composition and structure. The best way
engineering. Only the imagination limits the possibilities
to avoid these problems is to use molecules with the highest
available to the interested researcher. Figure 2 shows
possible purities.
schematic diagrams of several possible applications for
Table 2. ESCA composition data from PEG4 thiol monolayers with and
alkanethiol monolayers. These types of applications will likely
without “impurities” rescaled without gold signal. All data is shown in rely on high purity alkanethiols with head groups such as

of Pure Alkanethiols
Monolayers: Advantages
Self-Assembled
atomic percent. Two analysis spots are shown for each sample. The values those listed in Table 3.
in bold are the calculated atomic percentages based on the solution mixture
ratio of the compounds used.

Sample= C 1s O 1s S 2p
PEG4thiol (100%) 76.0 22.5 1.5

PEG4thiol 100% 74.7 23.9 1.4

PEG4thiol (100%-predicted) 76.0 20.0 4.0

PEG4thiol/TAA (99%/1%) 74.0 22.9 3.0

PEG4thiol/TAA (99%/1%) 73.7 22.7 3.7

PEG4thiol/TAA (99%/1%-predicted) 75.7 20.1 4.2

PEG4thiol/TAA (90%/10%) 73.7 19.4 6.9

PEG4thiol/TAA (90%/10%) 72.4 21.3 6.3 Figure 2. Possible applications for alkanethiol monolayers.
A) Non-fouling surfaces B) SAMs with specific binding receptors C) Cell
PEG4thiol/TAA (90%/10%-predicted) 73.4 20.5 6.1 supports for native cell growth and studies D) Molecular electronics
E) Microarrays F) Separations.
TAA (100%-predicted) 50 25 25

O r d e r :
=
PEG4 thiol = (1-mercapto-11-undecyl)tetra(ethylene glycol); Aldrich Table 3: Some head group examples useful for the applications
Prod. No. 674508 TAA = thioacetic acid shown in Figure 2.

Application Common Head Group

Results similar to these were seen when thioacetic acid was
Non-fouling surfaces PEGn, Mannose

1 . 8 0 0 . 3 2 5 . 3 0 1 0
present in PEG3 and PEG6 thiol samples. Both of these samples
showed a higher than expected gold and sulfur signals Specific binding receptors Biotin, NTA, Peptide,
indicating the layers were disordered and a sulfur contaminant Carbohydrates
was present. The most important property of poly(ethylene Cell supports Peptide
glycol) alkanethiols (PEGn thiols) is the ability to form a non- Molecular electronics CH3, SH
fouling self-assembled monolayer, but the presence of just Microarrays DNA, Peptide, PEGn
small amounts of carboxylic acid-terminated PEGn thiols
Separations NTA
(possibly introduced from poly(ethylene glycol) starting
material) leads to significant protein adsorption, making Surface reactions Azide, COOH, NH2, OH, SH
Te c h n i c a l

the surface more fouling than bare gold itself, as shown by

Roberts et al.9
The interference of thiol contamination with monolayer
formation has also been reported for the assembly of thiolated
DNA on gold.10 It was found that the presence of a thiol
contaminant, dithiothreitol, impeded the assembly of the
References:
(1) Nuzzo, R. G.; Allara, D. L. J. Am. Chem. Soc. 1983, 105, 4481. (2)
Strong, L.; Whitesides, G. M. Langmuir 1988, 4, 546. (3) Dubois, L. H.;
Nuzzo, R. G. Annu. Rev. Phys. Chem. 1992, 43, 437. (4) Bain, C. D.;
Whitesides, G. M. J. Am. Chem. Soc. 1989, 111, 7164. (5) Bain, C. D.;
Whitesides, G. M. Angew. Chem. Int. Ed. 1989, 28, 506. (6) Porter, M. D.;
S e r v i c e :

thiolated DNA onto the gold surface. The authors showed that
when contaminated thiolated DNA was used for the assembly,
the atomic percentages of characteristic DNA elements (P, N)
did not increase with increasing assembly times as they did
with purer samples. Increased assembly times instead resulted
Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109,
3559. (7) Bain, C. D.; Evall, J.; Whitesides, G. M. J. Am. Chem. Soc. 1989,
7155. (8) Nelson, K. E.; Gamble, L.; Jung, L. S.; Boeckl, M. S.; Naeemi, E.;
Golledge, S. L.; Sasaki, T.; Castner, D. G.; Campbell, C. T.; Stayton, P. S.
Langmuir 2001, 17, 2807. (9) Roberts, B. J.; Naeemi, E.; Ratner, B. D. JURBIE
2004, 4, 103-107. (10) Lee, C.-Y.; Canavan, H. E.; Gamble, L. J.; Castner,
1 . 8 0 0 . 2 3 1 . 8 3 2 7

in increased amounts of the contaminant molecules on the
surface. Samples prepared from relatively pure DNA showed
logical trends for the DNA elements in a time series assembly.
D. G. Langmuir 2005, 21, 5134. (11) Love, J. C.; Estroff, L. A.; Kriebel, J. K.;
Nuzzo, R. G.; Whitesides, G. M. Chem. Rev. 2005, 105, 1103. (12) Chaki, N.
K.; Vijayamohanan, K. Biosensors & Bioelectronics 2002, 17, 1. (13) Ulman,
A. Chem. Rev. 1996, 96, 1533.

For questions, product data, or new product suggestions,

please contact the Materials Science team at matsci@sial.com.
 

Alkane Thiols – Linear Chain

R-CH2(CH2)n-2CH2-SH

For package sizes and prices of products in this matrix, please visit sigma-aldrich.com.
n\Head Group (-R) -H -OH -COOH -SH (Dithiols)
3 P50757 (99%) 405736 (95%) M5801 (99+%)
4 451878 (95%)
5 P7908 (98%)
6 234192 (95%) 451088 (97%) 674974 (90%) H12005 (96%)
7 H4506 (95%)
Self-Assembled

of Pure Alkanethiols
Monolayers: Advantages

471836 (98.5%), O3605 (97+%),

8 675075 (96%)
662208 (*NanoThInksTM) 662615 (*NanoThInksTM)
9 674273 (99%), N31400 (95%) N29805 (95%)
10 D1602 (96%)
674249 (99%), 674427 (99%),
11 510467 (98%) 447528 (97%), 450561 (95%), 674281 (99%)
662224 (*NanoThInksTM) 662925 (*NanoThInksTM)
12 471364 (98+%) 675067 (96%)
14 87193 (98+%)
15 516295 (98%) 675091 (97%)
674435 (99%),
674516 (99%),
16 448303 (90%), 674400 (99%)
H7637 (92%)
662216 (*NanoThInksTM)
O1858 (98%),
18
662194 (*NanoThInksTM)
*NanoThInksTM are 5 mM solutions of the alkane thiol in high purity ethanol. NanoThInksTM is a trademark of Sigma-Aldrich Biotechnology, L.P.

Alkane Thiols – Branched, Fluorinated, or Other Terminal Groups

Alkane Thiol Structure Purity, % Product No.
1-Mercapto-2-propanol  CH3CHCH2SH 95 328375-1G 22.60
328375-5G 61.80
OH

Methyl 3-mercaptopropionate  O 98 108987-100G 29.50

H3CO C CH2CH2SH 108987-500G 79.50
108987-5G 20.60
3-Mercapto-2-butanol, mixture of isomers  OH 97 264792-1G 28.00
CH3CHCHCH3 264792-5G 93.30
SH

Butyl 3-mercaptopropionate O 98% 381454-100ML 22.90

C4H9O C CH2CH2SH 381454-500ML 54.30

3-(Dimethoxymethylsilyl)-1-propanethiol  OCH3 95 446173-10ML 18.00

CH3SiCH2CH2CH2SH 446173-50ML 50.00
OCH3

(3-Mercaptopropyl)trimethoxysilane  OCH3 95 175617-25G 18.70

CH3O Si CH2CH3CH3SH
s i g m a - a l d r i c h . c o m

OCH3

1H,1H,2H,2H-Perfluoro-1-hexanethiol CF3(CF2)2CF2
SH 98 16494-250MG 130.00

4-(6-Mercaptohexyloxy)benzyl alcohol HS(H2C)6 OH 96.5 673560-50MG 157.00

O

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call 1-800-325-3010 (USA), or visit sigma-aldrich.com/matsci.
 US $ 

Alkane Thiol Structure Purity, % Product No.

2-Ethylhexanethiol SH 96 669148-25G 34.60
669148-100G 112.50

tert-Nonyl mercaptan, mixture of isomers  CH3 CH3 97 171034-250ML 26.90

CH3 C CH2 C CH2SH 171034-1L 74.60
CH3 CH3

tert-Dodecylmercaptan, mixture of isomers  98.5 471585-100ML 16.00

C12H25SH 471585-500ML 28.80
471585-2L 55.40
1H,1H,2H,2H-Perfluorodecanethiol  97 660493-25G 157.00
CH2(CH2)6CH3
Au S 660493-5G 58.70

of Pure Alkanethiols
Monolayers: Advantages
Self-Assembled
11-Amino-1-undecanethiol, hydrochloride HS
NH2 HCl 99 674397-50MG 264.00

11-Mercaptoundecyl phosphoric acid O 99 674311-50MG 300.00

P
HO O
HO SH

11-Mercaptoundecyl trifluoroacetate O 99 674230-50MG 314.50

F3C O
SH

2,2’-(Ethylenedioxy)diethanethiol   HSCH2CH2OCH2CH2OCH2CH2SH 95 465178-100ML 18.00

465178-500ML 57.60
11-Mercaptoundecyl)tri(ethylene glycol) HS O O 95 673110-250MG 113.00
O OH

(1-Mercaptoundec-11-yl)tetra(ethylene O O
95 674508-250MG 129.00
glycol)l HS O O OH

(1-(Methylcarbonylthio)undec-11- O
O O
95 674176-250MG 91.90
H3C S O O OH
yl)tetra(ethylene glycol)
(1-Mercaptoundec-11-yl)hexa(ethylene HS O
O
O
O
O
O
OH 96.5 675105-250MG 270.80
glycol)
Hexa(ethyleneglycol)mono-11- O
O O O
95 675849-250MG 75.10
H3C
(acetylthio)undecylether S

O r d e r :
O O O OH

1 . 8 0 0 . 3 2 5 . 3 0 1 0

O ur NanoThinksTM solutions will help you get results faster by reducing prep time and
mixing errors. We feature our best selling thiol materials in a high-purity ethanol. Just
Te c h n i c a l

select the head group of the thiol and prepare your film. NanoThinksTM are ideal for use in
molecular assembly or dip-pen nanolithography applications. (The NanoThinksTM products are shown
on page 6 in the Alkane Thiols – Linear Chain Table.)

Visit our Web site at sigma-aldrich.com/selfassembly for more information and for our
S e r v i c e :

complete line of products for molecular self-assembly or email matsci@sial.com with

questions.
1 . 8 0 0 . 2 3 1 . 8 3 2 7

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Displaceable Monolayers and Microdisplacement Printing:
1-Adamantanethiol Assembly and Applications
Thomas J. Mullen, J. Nathan Hohman,
Dr. Arrelaine A. Dameron,
Jennifer R. Hampton, Susan D. Gillmor,
and Prof. Paul S. Weiss (photo)
Departments of Chemistry and Physics,
The Pennsylvania State University
Introduction
Self-assembly techniques at the supramolecular 1–100 nm
Microdisplacement
Printing
scale have been extensively studied for applications ranging
from biocompatible systems to microelectronics.1, 2 As the
dimensions of patterned surface structures decrease, the
difficulty and intricacy of fabricating and measuring these
structures increases.3, 4 Employing a library of molecules
with a range of distinctive chemical and physical properties
allows the design and the fabrication of thin films for specific
applications. 1-Adamantanethiol (1-AD), an example in this
spectrum of molecules with distinct chemical and physical
properties, forms self-assembled monolayers (SAMs) on
Au{111} that are displaceable when exposed to other thiolated
molecules from solution, vapor, or contact5, 6 due to weak
intermolecular interactions in 1-AD SAMs. This process is called
microdisplacement. The process can be applied to intelligent
self- and directed- assembly7, 8 to fabricate nanoscale-
separated SAMs and improve chemical patterning techniques.
Experimental
All SAMs were fabricated using 1-adamantanethiol (1-AD,
Aldrich Prod. No. 659452), 1-dodecanethiol (C12, Aldrich
Prod. No. 471364), and 1-octanethiol (C8, Aldrich Prod.
No. 471836) on commercially available Au{111} that was
evaporated onto freshly cleaved mica substrates and annealed
using a hydrogen flame just prior to deposition. A single
component 1-AD SAM was created by immersing a gold
substrate into a 10 mM ethanolic 1-AD solution for 24 h.
Subsequently, the gold substrate with the single-component
1-AD SAM was rinsed in neat ethanol and blown dry with
nitrogen twice.
To fabricate separated C12 and 1-AD SAMs, a single-
component 1-AD SAM was immersed in a 1 mM ethanolic
C12 solution for a displacement time of 20 min and then
rinsed in neat ethanol and blown dry with nitrogen twice.
Representative scanning tunneling microscopy (STM) images
were acquired for both the single-component 1-AD SAMs
and the separated C12 and 1-AD SAMs within 24 h of SAM
fabrication. From the STM images, the lattice structure, the
domain boundaries, and the molecular order of the SAMs
were investigated. All STM measurements were performed
under ambient conditions using a custom beetle-style STM.9
Images were recorded in constant-current mode and at high
tunneling gap impedances (~1012 GΩ) to ensure large tip-
s i g m a - a l d r i c h . c o m
sample separation for minimal contact between the probe tip
and the monolayer.
Microdisplacement-printed SAMs were fabricated by
contact of a C8 coated patterned elastomeric stamp with a
preformed single-component 1-AD SAM.7, 8 An elastomeric
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polydimethylsiloxane (PDMS) stamp was fabricated, cleaned,
and exposed to a 10 mM ethanolic solution of C8 for
10 s and blown dry with nitrogen using a modified method
described by Graham et al.10 The stamp with C8 ink was
contacted to the single-component 1-AD SAM for 5 min, and
then the sample was rinsed in neat ethanol and blown dry
with nitrogen twice. Lateral force microscopy (LFM) images
were acquired within 1 h of pattern fabrication using a
Thermo Microscopes Autoprobe CP Research Atomic Force
Microscope (Veeco, Santa Barbara, CA). Silicon nitride tips
with a spring constant of 0.05 nN/m were used as received
from Mikromasch (Portland, OR).
Results and Discussion
Ordered 1-AD monolayers were formed when a Au{111}
substrate was exposed to an ethanolic 1-AD solution.5
Figure 1 (A) displays a representative STM image of a single-
component 1-AD SAM predominantly showing two flat
terraces with several monatomic substrate step edges as well
as depressed regions attributed to substrate vacancy islands.
6.9
A
Ångstroms
250 Å
0.0
2.2
B
Ångstroms
50 Å
0.0
Figure 1. Scanning tunneling microscopy image of a 24 h
1-adamantanethiolate (1-AD) SAM on a Au{111} substrate. Image
parameters: Vsample = -0.75 V, Itunnel = 3.0 pA. A)
Resolution: 750 Å × 750 Å; shows several monatomic step edges and
substrate vacancy islands. B) Resolution: 200 Å × 200 Å; molecular
resolution shows the 1-AD lattice.
Both of these features are commonly observed in thiol
SAMs. Additionally, 1-AD SAMs show depressed domain
boundaries resulting from rotational domains of the 1-AD
molecules. This is in contrast to alkanethiolate SAM systems,
which exhibit protruding domain boundaries associated
with regions of molecules with differing tilts, rotational and
translational boundaries, and stacking faults.11-13 Figure 1 (B)
shows a representative STM image with molecular resolution
of a single-component 1-AD SAM, showing individual
molecules arranged in a hexagonally closed-packed structure
with nearest-neighbor spacing of 6.9 ± 0.4 Å. This lattice
spacing is considerably larger than the nearest-neighbor
spacing for alkanethiolate SAMs and can be attributed to
the bulky carbon cage of 1-AD molecules compared to the
relatively compact (predominantly all-trans) alkyl chains of

alkanethiolates. A (7×7) unit cell can be assigned to the 1-AD
SAM with respect to the Au{111} substrate.5 Typical alkanethiol
SAMs exhibit a (√3×√3)R30° unit cell. This implies that there
are 1.8 times more molecules in an alkanethiol SAM than in
a 1-AD SAM in the same area of Au{111}. For example, in a
(7√3×7√3)R30° unit area of Au{111}, which is the unit area
where the 1-AD and alkanethiolate unit cells overlap, there are
49 alkanethiolate molecules (21.4 Å2/molecule) and 27 1-AD
molecules (38.9 Å2/molecule).
Nanoscale-separated SAMs offer excellent opportunities to
investigate the influence of intermolecular interactions on
the assembly of thin films, which is essential for the further
development of chemical patterning techniques.14, 15 Figure 2
(A and B) show representative STM images of separated C12
and 1-AD SAMs formed via C12 solution displacement of
preformed 1-AD SAMs.
7.1
A
Ångstroms
250 Å
0.0
5.7
B
Ångstroms
50 Å
0.0
Figure 2. Scanning tunneling microscopy image of a separated
1-dodecanethiolate (C12) and 1-adamantanethiolate (1-AD) SAM on a
Au{111} substrate. Image parameters: Vsample = -1.20 V, Itunnel = 1.0 pA.
A) Resolution: 1000 Å × 1000 Å; shows distinct domains of both lattice
types: C12 - more protruding molecular domains; 1-AD - less protruding
molecular domains; the most depressed regions are substrate vacancy
islands. B) Resolution: 300 Å × 300 Å; shows the molecular order of each
lattice type.
The apparent heights and the differences in lattice spacing
were employed to differentiate between the C12 and
1-AD lattice types. The most protruding lattice with smaller
molecular spacing that originates at the substrate defects
was attributed to C12, while the less protruding lattice with
larger molecular spacing was attributed to 1-AD. Substrate
step edges and substrate vacancy islands (the most depressed
regions) were observed throughout the separated SAM. The
fractional C12 coverage of the separated C12 and 1-AD SAM
was controlled by the C12 displacement time (i.e. longer C12
displacement times result in larger C12 domains). At long
C12 displacement times, the resulting SAM was completely
composed of C12 molecules, although the C12 domains were
significantly smaller when compared to a single-component
C12 SAM.
Microcontact printing (µCp) is a technique for chemically
patterning a substrate by contact with an elastomeric
stamp that is inked with the molecules to be patterned.16
Molecules on the stamp are transferred from the stamp to
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please contact the Materials Science team at matsci@sial.com.
US $ 
the substrate only in places where the stamp and substrate
are in contact. However, this process is limited to molecules
that are not susceptible to lateral diffusion across the
surface. Microdisplacement printing (µDp), is an alternative
patterning technique not limited by lateral diffusion. In µDp,
a preformed 1-AD monolayer is used that is sufficiently labile
to be displaced by patterned molecules through competitive
adsorption while preventing lateral diffusion of the patterned
molecules.7,8 Figure 3 displays a LFM image of a patterned
Au{111} substrate fabricated by µDp.
Printing
Microdisplacement
10 µm
Figure 3: Lateral force microscopy (LFM) image of a patterned Au{111}
substrate made by microdisplacement printing. The low-friction (shown
as dark) squares are the stamped octanethiol molecules, and the high-
friction (shown as light) background is the preformed 1‑adamantanethiolate
SAM. Image parameters: 40 µm × 40 µm, Scan rate = 1.0 Hz, Force 
setpoint = 4 nN.
The low-friction (shown as dark) squares are stamped C8
O r d e r :
molecules, and the high-friction (shown as light) background
is the preformed 1-AD SAM. This pattern could not be formed
using traditional µCp printing. µDp also eliminates the need
for solvent exposure after stamping. Solvent exposure is
1 . 8 0 0 . 3 2 5 . 3 0 1 0
often required in µCp to prevent degradation of the pattern
over time, but the precision of the pattern is reduced due to
molecular exchange. With microdisplacement printing, the
1-AD SAM is still present in places where the elastomeric
stamp did not contact the surface; thus, a solvent exposure
step is not necessarily required. Multiple stamping steps can
also be used to create proximate structures, circumventing the
difficulty in the precise registration of neighboring patterns in
conventional printing.8
Te c h n i c a l
Conclusions
Highly ordered, one-molecule-thick films of 1-adamantanethiol
(1-AD) can be fabricated on Au{111} substrates. Exploiting
the labile nature of 1-AD SAMs, precise nanoscale-separated
SAMs can be fabricated and can enhance common chemical
S e r v i c e :
patterning techniques by hindering the lateral movement of
molecules across a patterned surface.
Acknowledgments
The Air Force Office of Scientific Research, Army Research
1 . 8 0 0 . 2 3 1 . 8 3 2 7
Office, Defense Advanced Research Projects Agency, National
Science Foundation, Office of Naval Research, Semiconductor
Research Corporation, and Sigma Aldrich are gratefully
acknowledged for their support.
 10

References
(1) Jeon, N. L.; Clem, P. G.; Nuzzo, R. G.; Payne, D. A., J. Mater. Res.
1995, 10, 2996. (2) Chen, C. S.; Mrksich, M.; Huang, S.; Whitesides,
G. M.; Ingber, D. E., Biotechnol. Prog. 1998, 14, 356. (3) Handbook of
Microlithography, Micromachining, and Microfabrication. SPIE: London,
1997. (4) Xia, Y. N.; Rogers, J. A.; Paul, K. E.; Whitesides, G. M., Chem.
Rev. 1999, 99, 1823. (5) Dameron, A. A.; Charles, L. F.; Weiss, P. S., J. Am.
Chem. Soc. 2005, 127, 8697. (6) Dameron, A. A. Controlling Molecular
Assemblies. The Pennsylvania State University, University Park, 2006. (7)
Dameron, A. A.; Hampton, J. R.; Smith, R. K.; Mullen, T. J.; Gillmor, S. D.;
Weiss, P. S., Nano Lett. 2005, 5, 1834. (8) Dameron, A. A.; Hampton, J.
R.; Gillmor, S. D.; Hohman, J. N.; Weiss, P. S., J. Vac. Sci. Technol., B 2005,
23, 2929. (9) Bumm, L. A.; Arnold, J. J.; Charles, L. F.; Dunbar, T. D.; Allara,
D. L.; Weiss, P. S., J. Am. Chem. Soc. 1999, 121, 8017. (10) Graham, D.
J.; Price, D. D.; Ratner, B. D., Langmuir 2002, 18, 1518. (11) Delamarche,
E.; Michel, B.; Gerber, C.; Anselmetti, D.; Guntherodt, H. J.; Wolf, H.;
Ringsdorf, H., Langmuir 1994, 10, 2869.
(12) Sellers, H.; Ulman, A.; Shnidman, Y.; Eilers, J. E., J. Am. Chem. Soc.
1993, 115, 9389. (13) Ulman, A.; Eilers, J. E.; Tillman, N., Langmuir 1989,
5, 1147. (14) Lewis, P. A.; Donhauser, Z. J.; Mantooth, B. A.; Smith, R. K.;
Bumm, L. A.; Kelly, K. F.; Weiss, P. S., Nanotechnology 2001, 12, 231.
(15) Smith, R. K.; Lewis, P. A.; Weiss, P. S., Prog. Surf. Sci. 2004, 75, 1.
(16) Wilbur, J. L.; Kumar, A.; Kim, E.; Whitesides, G. M., Adv. Mater. 1994,
6, 600.

Thiol Products
Product Description Structure Purity,% Product No.
Microdisplacement
Printing

1-Adamantanethiol  SH 95 659452-5G 55.50

H
H
H

Biphenyl-4,4′-dithiol  HS SH
95 673099-1G 95.00

Alkane Disulfides
Alkane Disulfide Structure Purity,% Product No.
Undecyl disulfide S 99 674303-250MG 180.00

Hydroxyundecyl disulfide OH
99 674257-250MG 220.00
S

OH

Carboxy undecyl disulfide O

OH
99 674451-250MG 157.00
S
OH

O S

Hexadecyl disulfide S 99 674419-500MG 157.00

S

Hydroxyhexadecyl disulfide OH
S
99 674478-100MG 220.00
OH
S

Carboxy hexadecyl disulfide O

OH
99 674443-250MG 220.00

OH S
S
O

Gold Surfaces and Sources for Self-Assembly

Product Description Coating Thickness/Particle Size Prod. No.
99.999% Gold coated silicon wafer, 4”× 500 μm wafer 1000 Å 643262-1EA 123.50
99.999% Gold coated microscope slide, 3”×1”× 0.7 mm slide 100 Å 643203-5EA 243.50
99.999% Gold coated microscope slide, 3”×1”× 0.7 mm slide 1000 Å 643246-5EA 371.50
Gold coated glass cover slip, 22 mm x 22 mm square 100 Å 643254-12EA 391.00
643254-24EA 416.50
Gold coated glass cover slip, 15 mm diameter 100 Å 643289-24EA 480.50
Gold coated mica, 1”x 3” slide 2000 Å 643297-1EA 737.00
Gold colloid 3.5–6.5 nm G1402-25ML 63.40
Gold colloid 8–12 nm G1527-25ML 63.40
s i g m a - a l d r i c h . c o m

Gold colloid 17–23 nm G1652-25ML 63.20

Gold, nanopowder, 99.9+% 50–130 nm 636347-1G 203.00
Gold, wire, 1.0 mm diameter, 99.999% 1.0 mm† 349305-1.5G 260.50
349305-375G 83.90
Gold surface cleaning solution 667978-500ML 33.50
†
Wire diameter. For additional gold products, visit sigma-aldrich.com/matsci.

TO ORDER: Contact your local Sigma-Aldrich office (see back cover),

call 1-800-325-3010 (USA), or visit sigma-aldrich.com/matsci.

Self-Assembly In Organic Thin Film Transistors
For Flexible Electronic Devices
Professor Zhenan Bao
Department of Chemical Engineering,
Stanford University
Introduction
Flexible electronic circuits and displays based on organic
active materials are future generations of products that
may eventually enter mainstream electronics market. The
advantages in using organic active materials are their ease in
tuning electronic and processing properties by chemical design
and synthesis, low cost processing based on low temperature
processes and reel-to-reel printing methods, mechanical
flexibility, and compatibility with flexible substrates.1
Organic thin film transistors (OTFTs) are the basic building
blocks for flexible integrated circuits and displays. A schematic
structure is shown in Figure 1.2
Figure 1. Schematic structure of an organic thin film transistor.
(a) Chemical structure of the silane molecule used as the self-assembled
monolayer dielectric layer (b) Chemical structure of pentacene used as
the semiconductor layer (c ) schematic structure of the device. Reproduced
with permission from the Nature Publishing Group.
During the operation of the transistor, a gate electrode is used
to control the current flow between the drain and source
electrodes. Typically, a higher applied gate voltage leads to
higher current flow between drain and source electrodes. A
fast switching transistor should have a high charge carrier
mobility and a high on/off current ratio for the semiconductor
material. For the pixel switching transistors in liquid crystal
displays, mobility greater than 0.1 cm2/Vs and on/off ratio
greater than 106 are needed.
Both self-assemblies and self-assembly processes play
important roles in improving device performance as well as
enabling low cost processing methods for the fabrication of
these devices. In this article, a briefly survey is given on the
applications of self-assembly in OTFTs.
For questions, product data, or new product suggestions,
please contact the Materials Science team at matsci@sial.com.
US $ 11
Surface modification with self-assembled
monolayers (SAMs)
Drain and source electrode surface modification with
SAMs
For organic transistors to function well, charge injection from
the electrode needs to be efficient. This requires the work
function of the electrode to match well with the energy level
of the organic semiconductor such that the energy barrier
for charge injection is low. For organic transistors, typically
high work function electrodes (Au, Pd, or indium tin oxide)
have been used for p-channel organic semiconductors, in
Electronics
Self-Assembly in Flexible
which holes are injected and transported through the organic
material. It has been found that electrode surface modification
with a self-assembled monolayer can be used to improve the
charge injection into the organic semiconductor.3 For example,
when Au electrodes are used, they can be functionalized with
various thiol SAMs to tune their work functions. Moreover, the
morphology of organic semiconductors is significantly different
when deposited on SAM modified Au compared to bare Au.
This observation has been used to tune the morphology of the
organic semiconductor at the Au/organic interface to improve
its charge injection.4
Dielectric surface modification
Surface treatment of dielectric layer is an important way
to improve organic transistor performance. Since most of
the charge carriers induced in the semiconductor layer are
confined to the first 5 nm of organic semiconductor from
the semiconductor/dielectric interface, the dielectric surface
chemical and physical characteristics thus play a significant role
on the charge carrier transport. For example, Si-OH groups
O r d e r :
on SiO2 surface (a typical dielectric material) is known to trap
electrons. Capping SiO2 surfaces with octadecyl trichlorosilane
(OTS) molecules can significantly reduce electron traps and
improve mobility of n-channel semiconductors (electrons are
the major charge carriers).5
1 . 8 0 0 . 3 2 5 . 3 0 1 0
Additionally, dielectric surface treatment with SAMs also
affects the nucleation and growth of organic semiconductors.6
For example, pentacene is an organic semiconductor with the
highest reported thin film charge carrier mobility. Its charge
carrier mobility changes significantly depending on the types
of hydrophobic SAM surface treatment. This difference is
related to the morphological difference of the first pentacene
monolayer formed on different surfaces.6
Te c h n i c a l
SAMs as the active dielectric or semiconductor
layers
Dielectric layer
The dielectric layer for organic transistors should be as thin
S e r v i c e :
as possible, pinhole-free, and ideally with a high dielectric
constant for low voltage operation. A well-ordered densely
packed SAM may be the thinnest possible high quality
dielectric layer. As shown in Figure 1, a SAM is used as the
active dielectric layer for high performance low voltage organic
1 . 8 0 0 . 2 3 1 . 8 3 2 7
transistors.2 Other SAMs, as well as self-assembled multilayers,
have also been reported as high performance dielectric layers
Figure 2.7,8 SAM initiators have been used for initiating
surface polymerization to form dielectric layers Figure 3.9
 12
Self-Assembly in Flexible
Electronics

Figure 2. Schematic representation of the components of an OTFT showing the molecular structures of various organic semiconductors (left) and self-
assembled nanodielectries I-III (right). Nanodielectric layers were deposited from solutions of silane precursors.

S Catalyst S [Ru] Monomer S

Solution Solution [Ru]
Au Au Au

Ph Ph
S S [Ru] X
[Ru]

Ph Ph
Au Au
Semiconductor
Deposit Semiconductor, Polymer Dielectric
Drain / Source Electrodes
Au
Au

Si / SiO2

Figure 3. Modification of a gold gate electode for the surface initiated polymerization reaction to grow a dielectric layer.

Semiconductor layer Self-assembled monolayers for patterning

To facilitate charge transport, the organic semiconductor layer
usually comprises of pi-conjugated oligomers or polymers,
in which the pi-pi stacking direction should ideally be along
the current flow direction. This requires the semiconductor
molecules to self-assemble into desirable orientation upon
either vapor or solution deposition. These well-ordered
molecular layers can be formed by (1) proper molecular design
of chemical structures that favor crystallization into large
ordered domains or (2) self-assembly into mono and multi
layers.10,11
Regioregular poly(3-hexylthiophene) is one of the few polymer
semiconductors that spontaneously assemble into well ordered
structures upon solution deposition by drop casting or spin
coating Figure 4.12 It is among the few reported polymer
semiconductors with a mobility greater than 0.1 cm2/ Vs.13,14
Layer-by-layer deposition is a potentially useful method for
s i g m a - a l d r i c h . c o m
For organic transistors, the active semiconductor layer has to
be patterned in order to minimize cross talk between devices.
Additionally, both the drain and source electrodes need to
be patterned so that they are separated by at most a few
micrometers depending on application requirements.
In addition to various printing methods, such as ink-jet
printing, screen printing, and offset printing,15-17 SAM
modified surfaces have been used for selective deposition
of organic semiconductors through patterned wettability or
templated growth Figure 5.18,19 Patterned SAM layers can be
patterned by conventional photolithography or microcontact
printing.20 In addition to pattern organic semiconductors,
patterned SAM can be used as an etch resistant layer to
prevent etching of an Au film underneath a thiol SAM to
generate Au electrodes.21 Patterned SAM layers have also
been used to initiate electroless plating of patterned metal

organic semiconductor deposition. It allows precise control electrodes on plastic substrates.22

of the layer thickness, roughness, chemical composition,
and molecular orientation. This method has been used to
prepare self-assembled multilayers of copper phthalocyanine
derivatives. Ion-assisted doping has been observed for these
devices.11

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call 1-800-325-3010 (USA), or visit sigma-aldrich.com/matsci.
 US $ 13

In summary, both self-assemblies and self-assembly processes

are crucial as active materials as well as low cost fabrication
methods for organic flexible electronic devices. Significant
progress has already been made in this field. Nevertheless,
as the demand for performance and precision in patterning
increases, self-assembly processes will become increasingly
important.
References:
(1) Ling, M. M.; Bao, Z. N. Chem. Mat. 2004, 16, 4824. (2) Halik, M.;
Klauk, H.; Zschieschang, U.; Schmid, G.; Dehm, C.; Schutz, M.; Maisch, S.;
Effenberger, F.; Brunnbauer, M.; Stellacci, F. Nature 2004, 431, 963.
(3) Gundlach, D. J.; Jia, L. L.; Jackson, T. N. IEEE Electr. Dev. 2001, 22, 571.
(4) Kymissis, I.; Dimitrakopoulos, C. D.; Purushothanman, S. IEEE Trans. Elec.
Dev. 2001, 48, 1060. (5) Chua, L. L.; Zaumseil, J.; Chang, J. F.; Ou, E. C. W.;

Figure 4. Regioregular poly(3-hexylthiophene) spontaneously assemble into
ordered structures upon solution deposition. The pi-pi stacking between
polymer chains facilitates change transport.
a b
c d e Whitesides, G. M. Chem. Rev. 1999, 99, 1823. (21) Bao, Z.; Rogers, J. A.;
Electronics
Self-Assembly in Flexible
Ho, P. K. H.; Sirringhaus, H.; Friend, R. H. Nature 2005, 434, 194. (6) Yang,
H. C.; Shin, T. J.; Ling, M. M.; Cho, K.; Ryu, C. Y.; Bao, Z. N. J. Am. Chem.
Soc. 2005, 127, 11542. (7) Collet, J.; Tharaud, O.; Chapoton, A.; Vuillaume,
D. Appl. Phys. Lett. 2000, 76, 1941. (8) Yoon, M. H.; Facchetti, A.; Marks,
T. J. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 4678. (9) Rutenberg, I. M.;
Scherman, O. A.; Grubbs, R. H.; Jiang, W. R.; Garfunkel, E.; Bao, Z. J. Am.
Chem. Soc. 2004, 126, 4062. (10) Tulevski, G. S.; Miao, Q.; Fukuto, M.;
Abram, R.; Ocko, B.; Pindak, R.; Steigerwald, M. L.; Kagan, C. R.; Nuckolls,
C. J. Am. Chem. Soc. 2004, 126, 15048. (11) Locklin, J.; Shinbo, K.; Onishi,
K.; Kaneko, F.; Bao, Z. N.; Advincula, R. C. Chem. Mat. 2003, 15, 1404.
(12) McCullough, R. D. Adv. Mater. 1998, 10, 93. (13) Bao, Z.; Dodabalapur,
A.; Lovinger, A. J. Appl. Phys. Lett. 1996, 69, 4108. (14) Sirringhaus, H.;
Tessler, N.; Friend, R. H. Science 1998, 280, 1741. (15) Sirringhaus, H.;
Kawase, T.; Friend, R. H.; Shimoda, T.; Inbasekaran, M.; Wu, W.; Woo, E. P.
Science 2000, 290, 2123. (16) Bao, Z. N.; Feng, Y.; Dodabalapur, A.; Raju,
V. R.; Lovinger, A. J. Chem. Mat. 1997, 9, 1299. (17) Zielke, D.; Hubler, A.
C.; Hahn, U.; Brandt, N.; Bartzsch, M.; Fugmann, U.; Fischer, T.; Veres, J.;
Ogier, S. Appl. Phys. Lett. 2005, 87. (18) Kagan, C. R.; Breen, T. L.; Kosbar,
L. L. Appl. Phys. Lett. 2001, 79, 3536. (19) Briseno, A. L.; Aizenberg, J.;
Han, Y. J.; Penkala, R. A.; Moon, H.; Lovinger, A. J.; Kloc, C.; Bao, Z. A. J.
Am. Chem. Soc. 2005, 127, 12164. (20) Xia, Y. N.; Rogers, J. A.; Paul, K. E.;
Katz, H. E. J. Mater. Chem. 1999, 9, 1895. (22) Zschieschang, U.; Klauk, H.;
Halik, M.; Schmid, G.; Dehm, C. Adv. Mater. 2003, 14, 1147.

O r d e r :
Figure 5. Optical micrographics of patterned arrays of organic
semiconductor crystals nucleated selectively on to self-assembled terphenyl

1 . 8 0 0 . 3 2 5 . 3 0 1 0
thiol template patterens: (a) and (b) anthracence crystals, scale bar = 200
mm; (c) large oriented sigle crystal of anthracene, scale bar = 50 mm (d)
patterned anthrancene crystalline films, scale bar = 300 mm; (e) patterned
single crystal of 5-chlorotetracence, scale bar = 100 mm

Alkyl Silanes – Linear Chain

CH3(CH2)n-2CH2-SiR3
Te c h n i c a l

For package sizes and prices of products in this matrix, please visit sigma-aldrich.com
n\-R -OCH3 -OCH2CH3 -Cl
3 175617 (95%)
5 533386 (99%)
6 446963 (97%)
S e r v i c e :

8 376221 (96%) 440213 (96+%)

10 448591 (97%)
12 44237 (95+%) 280569 (98%)
16 52360 (85%) 52356 (80%)
1 . 8 0 0 . 2 3 1 . 8 3 2 7

18 376213 (90%) 104817 (90%), 74762 (85+%)

For questions, product data, or new product suggestions,

please contact the Materials Science team at matsci@sial.com.
 14

Additional Silanes for Self-Assembly

Silane Structure Purity, % Product No.
(3-Aminopropyl)triethoxysilane  OCH2CH3 99 440140-100ML 37.60
CH3CH2OSiCH2CH2CH2NH2 440140-500ML 139.00
OCH2CH3

(3-Glycidyloxypropyl)trimethoxysilane  H3C
O
98 440167-100ML 26.80
Si
O
O 440167-500ML 88.70
O CH3 O
H3C

1H,1H,2H,2H-Perfluorooctyltriethoxysilane  F2
C
F2
C
F2
C
OCH2CH3 97 667420-25G 220.00
F3C C
F2
C
F2
Si OCH2CH3 667420-5G 68.10
OCH2CH3

Octenyltrichlorosilane, mixture of isomers  Cl 96 539279-25ML 162.00

H2C Si Cl
Self-Assembly in Flexible
Electronics

Cl

1H,1H,2H,2H-Perfluorodecyltriethoxysilane  CF3(CF2)7CH2CH2Si(OCH2CH3)3
97 658758-25G 178.50
658758-5G  45.30
Methoxy(dimethyl)octadecylsilane  CH3 >90 40955-100ML 325.00
CH3OSiCH2(CH2)16CH3
40955-25ML 119.00
CH3

Functionalized Nanoparticles for Self-Assembly

Product Description Structure Product No.
Octanethiol functionalized gold nanoparticles, CH2(CH2)6CH3
660426-5ML 357.50 
Au S
2 % (w/v) in toluene 
Dodecanethiol functionalized gold nanoparticles, CH2(CH2)10CH3 660434-5ML 357.50
Au S
2 % (w/v) in toluene
Dodecanethiol functionalized silver nanoparticles, CH2(CH2)10CH3
667838-25ML 126.00
Ag S
0.25 % (w/v) in hexane
3-Aminopropyl functionalized silica nanoparticles, Si
NH2 660442-25ML 141.50
3 % (w/v) in ethanol
3-Aminopropyl-(3-oxobutanoic acid) functionalized silica H
O 660450-25ML 188.50
N
Si OH
nanoparticles, 2.5 % (w/v) in DMF O

Functionalized Polyelectrolytes
Polyelectrolytes are defined as materials for which properties in solvents with high dielectric constant are governed by
electrostatic interactions over distances larger than typical molecular dimensions.1,2 These materials have been successfully
applied in electrostatic self-assembly techniques3 for thin film deposition of electrically conducting polymers,4 conjugated
polymers for light emitting devices,5 nanoparticles,6 and nonlinear optical (NLO) materials.

Sigma-Aldrich offers a comprehensive selection of polyelectrolytes, anionic and cationic. Visit sigma-aldrich.com/selfassembly.

New additions Product No.

Poly(fluorescein isothiocyanate allylamine hydrochloride)
­­­­­­­­­­­­­­­­­­­­­FITC Functionalized Polyelectrolyte 70K base polymer Mw 630209-250MG 215.00
FITC Functionalized Polyelectrolyte 15K base polymer Mw 630217-250MG 215.00
Poly(vinylphosphonic acid)  661740-1G 175.00
s i g m a - a l d r i c h . c o m

(1) Specialty Polymers; Dyson, R.W., Ed.; Chapman and Hall, 1987; p 110; Aldrich Prod. No. Z22,414-6. (2) For a discussion of the differences between
polyelectrolytes and ionomers, see: Eisenberg, A.; Kim, J-S. Introduction to Ionomers; John Wiley, 1998; Aldrich Prod. No. Z41,033-0. (3) Handbook of
Polyelectrolytes and Their Applications, 3 Volumes, Tripathy, S. et al., Eds.; American Scientific Publishers, 2002; Aldrich Prod No. Z54,718-2. (4) Sayre, C.N.;
Collard, D.M. J. Mater. Chem. 1997, 7, 909. (5) Cheung, J. et al. Polym. Prepr. 1993, 34, 757. (6) Schmitt, J. et al. Adv. Mater. 1997, 9, 61.

TO ORDER: Contact your local Sigma-Aldrich office (see back cover),

call 1-800-325-3010 (USA), or visit sigma-aldrich.com/matsci.

High Affinity Polyvalent NanotetherTM SAMs on Gold:
Why More is Better
Dr. Brenda D. Spangler, CEO,
Dr. E. Scott Tarter,
Dr. Benjamin D. Reeves,
Dr. Zhiyong Suo
SensoPath
Technologies, Inc.
Association of Sulfur with Gold
Self-assembled monolayers or SAMs of thiols and organic
disulfides on gold surfaces were described by Nuzzo and
Allara in 19831 as a considerable improvement over difficult
to maintain Langmuir-Blodgett monolayers. Extensive studies
by these authors and by the Whitesides group at Harvard
University led to a generally accepted conclusion that the
bonding state of an adsorbed thiol or disulfide on gold was
an Au-thiolate (Au0-S-) with a binding energy somewhere
between the binding energy for electrostatic interaction and
a covalent bond, based on X-ray-photoelectron spectroscopy
(XPS), Auger electron spectroscopy, temperature-programmed
desorption and high-resolution electron energy loss
spectroscopy 2–5. There is also indication that the disulfide
association is much faster and more stable than a simple
monothiol association with the gold surface, a point we
will return to later in this article, and that the S-S bond of a
disulfide may be cleaved during adsorption to the Au(111)
surface5 to yield the thiolate. On the other hand, an in-depth
X-ray diffraction study by Fentner et al.6 suggests that the
monolayer spacing (2.2 A°) of alkane thiols on Au(111) is close
enough to imply the existence of a disulfide bond between
adjacent alkane thiols. It is then possible to hypothesize that
the sulfur atoms may intercalate between the gold atoms,
thus accounting for the deprotonation of the thiol to thiolate
or disulfide and concomitant presence of Au0, as well as
enhanced binding energy and enhanced stability of the sulfur-
gold association beyond a simple electrostatic interaction.
More is Better
Polyvalent interactions are one of the basic concepts of
biological molecular recognition. Multiple ligand binding,
represented by polyvalent antibodies or oligomeric binding
subunits is characteristic of many bacterial toxins, as well
as several enzyme systems and the well known example in
molecular assembly, the tetrameric strepavidin interaction with
biotin. Multiple interactions provide a far stronger association
than the affinity (KA) of single ligand for its target substrate.
This point has been extensively explored7 and in fact, discussed
in terms of stability of alkane thiol monolayers, which
spontaneously desorbed in solvent under ambient conditions
from gold, silver, platinum, or copper. Both desorption and
self-exchange were observed although residual thiols that
could not be desorbed were observed8. The resulting patchy
surface, however, left significant areas of metal exposed. The
desorption-resorption phenomenon has been proposed as a
For questions, product data, or new product suggestions,
please contact the Materials Science team at matsci@sial.com.
US $ 15
mechanism for stochastic switching in wired molecules that
are part of an alkanemonothiol self-assembled monolayer9.
It is clear that stability of the monolayer could be improved
significantly by the simple construction of divalent or
polyvalent thiols. The reasoning is as follows: for uncorrelated
desorption of widely spaced adsorbing groups such as those
on a dithiolalkane phenyl ring, the adsorption can be treated
statistically. The probability of a polyvalent molecule, for
example, a Nanotether™, having all thiols off the gold surface
simultaneously (total desorption) is a power series. That is, if
the association constant ka = x for a monothiol, then ka = x2
for a dithiolalkane phenyl group. Imagine a group of monkeys
NanotethersTM
High Affinity Polyvalent
hanging by only one hand from a tree branch, reaching for a
banana in a wind flow. Any monkey who lets go will be blown
away without the banana. If the monkeys were hanging by
both hands while reaching for a banana with their tails, then
they would be exponentially more stable and much less likely
to be blown off the branch. Monkeys hanging by both hands
and their tails would, of course, be ka3 more stable.
Monothiol vs Dithiol Monolayers
Figure 1 shows that aromatic dithiol tethers (Aldrich Prod.
No. 674338) do in fact adsorb more quickly and provide more
surface coverage than aromatic monothiols (Aldrich Prod.
No. 673560). The data were recorded on a Reichert 7000
Surface Plasmon Resonance (SPR) instrument by flowing the
nanotethersTM (1 mM in 100% ethanol) over a clean gold SPR
slide then washing with 100% ethanol at a preset time.
30
25
O r d e r :
20
15
1 . 8 0 0 . 3 2 5 . 3 0 1 0
10
5
0
0 500 1000 1500 2000 2500
T i me (s)
HO
Te c h n i c a l
HO
O O
O
(CH2)6SH (CH2)6SH HS(H2C)6
Aldrich Prod. No. 674338 Aldrich Prod. No. 673560
S e r v i c e :
Figure 1. Monolayer formation by dithiol aromatic NanotetherTM (red) vs
monothiol aromatic NanotetherTM (blue) followed by solvent wash. Arrow
indicates introduction of 100% ethanol wash.
The dithiol adsorption is significantly faster and after
1 . 8 0 0 . 2 3 1 . 8 3 2 7
washing, the resulting dithiol monolayer has a higher
refractive index (higher pixel number) than the monothiol
dendron monolayer suggesting better coverage. We believe
the sharp drop upon initiation of ethanol wash is due to
 16
loss of unadsorbed dendrons accumulated on the saturated
monolayer surface. Non-specifically adsorbed films have been
previously observed when slides are pulled from solutions
containing thiols after set-up of the self-assembled monolayer.
Desorption and loss of the non-specifically adsorbed material
can be directly observed on a quartz crystal microbalance
or a surface plasmon resonance slide during washing of the
freshly prepared slide mounted in the appropriate instrument.
For 1:10 molar ratio of mixed self assembled monolayers
consisting of carboxyl-terminated and hydroxyl-terminated
thiol or dithiol nanotethersTM (see Figure 2), unpublished AFM
data (Suo, Z. Montana State University, Bozeman, personal
communication) indicated that monothiol alkane PEG mixed
self-assembled monolayers showed patches of bare gold
High Affinity Polyvalent
NanotethersTM
while dithiol aromatic PEG mixed monolayers appeared to
be homogeneous. XPS data for the same slides indicated
significantly more sulfur-gold interaction for the dithiol over
the monothiol mixed self-assembled monolayers.
The apparent stability of the dithiol mixed self-assembled
monolayer may account for the observation that the detection
ratio of Staphylococcus aureus binding compared to E. coli
binding for a dithiol surface ratio was 2.3, while for the
monothiol surface was 1.29, indicating greater selectivity
for the pathogen on the dithiol surface. In the same study,
nonspecific binding response was 133.3 for the monothiol
surface and 39 for the dithiol surface10.
Monothiol Mixed Self-assembled Monolayer
s i g m a - a l d r i c h . c o m
Dithiol Mixed Self-assembled Monolayer
Figure 2. Monothiol and dithiol mixed self-assembled monolayers with
PEGolated spacers.
TO ORDER: Contact your local Sigma-Aldrich office (see back cover),
call 1-800-325-3010 (USA), or visit sigma-aldrich.com/matsci.
Immobilization Strategies
Self-assembled monolayers provide the opportunity
for a variety of chemical strategies to be employed for
immobilization of specific ligands, for construction of a
non-fouling surface or for electrochemical applications. The
hydroxyl terminated dithiolalkane aromatic rigid-rod tether
(Nanotether BPA, Aldrich Prod. No. 674346) can be used as a
non-fouling SAM or for further functionalization. The carboxyl-
terminated Nanotether BPA-HA (Aldrich Prod. No. 674354)
in Figure 3 can be coupled to proteins, amino-terminated
DNA oligomers or any other amine-containing molecule
using standard EDC/NHS coupling chemistry11. It could be
used to provide a hydrophilic, negatively charged surface,
or further functionalized chemically. Hydrazide-terminated
tethers (Nanotether™ BPA-HH, Aldrich Prod. No. 674370)
in Figure 4 couple easily with any aldehyde, including
aldehydes generated from glycosylated antibodies by sodium
periodate11,12 resulting in specific orientation of the antibody
without impairing antibody activity, rather than the random
orientation that results from EDC/NHS coupling to carboxyl-
terminated tethers.
O O(CH2)5COOH
flexible spacer with
functionalized terminus
rigid rod module
O O
(CH2)6SH (CH2)6SH
hydrophobic module
Figure 3. A typical rigid-rod dithiol tether (NanotetherTM BPA-HA Aldrich
Prod. No. 674354).
Future Outlook
Monodisperse macromolecules including flexible linear, rigid-
rod and dendritic segments offer unique design capabilities
that allow positioning of a variety of ligands through
multivalent attachment functionalities while controlling the
ultimate flexibility of the tether. These types of constructs can
be functionalized for attachment to various surfaces and, on
their other terminus, functionalized for covalent coupling of
proteins, peptides, and small organic ligands, all of which can
be varied independent of one another and be connected to
each other through spacers with varying degrees of rigidity. A
hydroxyl terminus, for example Nanotether BPA (Aldrich Prod.
No. 674346) either alone or as part of a poly(ethylene glycol)
module, provides an excellent antifouling surface.
The rigid-rod (bisphenolA) modular construct shown in
Figure 3 contains a flexible alkane spacer with functional
terminus for attachment of ligand. In effect, it becomes a
“nano fishing rod” for many different assay applications in
which the ligand may be presented as if it were on a cell
membrane. A typical application is shown in Figure 4 in which
antibody capture ligand (the “bait”) has been covalently
coupled to immobilized hydrazide-terminated Nanotether
BPA-HH (Aldrich Prod. No. 674370). With a PEGolated spacer
module, the “line” would swing free in aqueous solvent, to
mimic solution-phase binding.
 US $ 17

The rigidity of the bisphenol A module on the tether makes it

0.01 M NalO4 an interesting choice for use with a quartz crystal microbalance
where it could be used to probe viscoelastic effects in a flow
CHO
O
OHC cell configuration. Atomic force microscopy applications
are another potential use for rigid-rod tethers, to prevent
O O
O
O
O

glycosylated antibody the coupled (or “bait”) ligand from swinging back onto the
+
AFM tip where it may become ensnared. Considering other
O O(CH2)5CONHNH2
modular approaches, it is possible to modify the thiol terminus
O O
by substituting orthopyridinium disulfide or other coupling
bait reagents, linking the NanotetherTM to carbon nanotubes
S S
through the carboxyl terminus, or through a triethoxysilane
terminus to provide a 3-point attachment for coupling
to glass. Applications are limited only by a researcher’s
imagination.
O(CH2)5CONHN:C References

Biosensor Program
Biotechnology
rod O
(1) Nuzzo, R.G.; Allara, D.L., J. Am. Chem. Soc. 1983, 105, 4481. (2) Bain,
line
O
C.D.; Biebuyck, H.A.; Whitesides, G.M., Langmuir 1989, 5, 723. (3) Bain,
O
C.D.; Troughton, E.B.; Tao, Y.-T.; Evall, J.; Whitesides, G.M.; Nuzzo, R.G.,
flexible arm J. Am. Chem. Soc. 1989, 111, 321. (4) Biebuyck, H.A.; Whiresides, G.M.,
S
Langmuir 1993, 9, 1766. (5) Nuzzo, R.G.; Zegarski, B.R.; Dubois, L.H., J.
S

Am. Chem. Soc. 1987, 109, 733. (6) Fenter, P.; Eberhardt, A.; Eisenberger, P.,
Science 1994, 266, 1216. (7) Mammen, M.; Choi, S.-K.; Whitesides, G.M.,
Figure 4. Tethering an oxidized antibody to a hydrazide-terminated tether
Agnew. Chem. Int. Ed. Engl. 1998, 37, 2754. (8) Schlenoff, J.B.; Li, M.; Ly,
H., J. Am. Chem. Soc. 1995, 117, 12528. (9) Ramachandran, G.K.; Hopson,
T.J.; Rawlett, A.M.; Nagahara, L.A.; Primak, A.; Lindsay, S.M., Science 2003,
300, 1413. (10) Subramanian, A.; Irudayaraj, J.; Ryan, T., Sensors and
Actuators B 2005, online www.sciencedirest.com, 1. (11) Hermanson, G.T.,
Bioconjugate Techniques. Academic Press: San Diego, 1996; p 785. (12)
Spangler, B.D.; Tyler, B.J., Anal. Chim. Acta 1999, 399, 51.
Polyvalent Alkane Thiols – NanotethersTM
Product Description Structure Purity,% Product No.
Nanotether OH HO
96.5 674338-50MG 150.00

O O
(CH2)6SH (CH2)6SH

Nanotether BPA HS(H2C)6 O

O OH
96.5 674346-50MG 250.00

HS(H2C)6 O

O r d e r :
Nanotether BPA-HA HS(H2C)6 O
O O(CH2)6COOH
96.5 674354-50MG 350.00

HS(H2C)6 O

Nanotether BPA-HH O
96.5 674370-50MG 367.00

1 . 8 0 0 . 3 2 5 . 3 0 1 0
O O
O(CH2)6CONHNH2
(CH2)6SH (CH2)6SH

TM
Nanotethers is a trademark of Sigma-Aldrich Biotechnology, L.P.

Research Biotechnology Biosensor Program

Sigma-Aldrich Research Biotechnology has recently signed a series of agreements that expands its position in the areas of RNA
Interference (RNAi), gene expression and cell-based assays. Sigma-Aldrich and Panomics (formerly Genospectra), a leading developer
of products to support systems biology, have signed several agreements in which Sigma-Aldrich has acquired a minority equity stake in
Te c h n i c a l

Panomics and has been granted access to various Panomics technologies.

Under the agreed upon terms Sigma-Aldrich gained access to Panomics’s unique nano-particle system for delivery of siRNA and other
biomolecules to cells. The companies will participate in a joint program to develop new technologies and products in the area of cell-
based assays, particularly to supply novel live cell biosensor assay reagents. These reagents provide real-time data on protein activity and
location in living cells, and will make an impact in the High Content Screening and Cell-Based Assay fields. David Lawrence, Ph.D. from
Albert Einstein College of Medicine and Klaus Hahn, Ph.D. from University of North Carolina, Chapel Hill, are two noteworthy scientists
S e r v i c e :

who are collaborating with Panomics and Sigma-Aldrich in this endeavor.

As Sigma-Aldrich expands its involvement in the area of cell-based assays, a focused business development approach is being
undertaken. Sigma-Aldrich welcomes the opportunity to license and/or acquire novel biosensors and biosensor technologies to provide
to the research community.
1 . 8 0 0 . 2 3 1 . 8 3 2 7

If you are interested in collaborating with us,

please feel free to contact us at sigma-aldrich.com/bd.
We look forward to hearing from you.

For questions, product data, or new product suggestions,

please contact the Materials Science team at matsci@sial.com.
 18
A Step-by-Step Guide for Solution
Based Self-Assembly
Dr. Dan Graham, Assemblon;
Dr. Sean Dingman,
Sigma-Aldrich
Self-assembled monolayers of thiols are prepared by immersion
of a clean gold substrate into a dilute solution of the desired
thiol. Although self-assembly takes place very quickly, good
experimental procedures are needed to produce highly ordered
Protocol for SAMs
Preparation
films. A recommended protocol for preparing SAMs is outlined
in this article.
Equipment and Materials
Equipment Checklist and Considerations
1. Gold coated substrates (See pg 10 for our substrates)
2. Thiol compound(s)
3. Fresh 200 proof ethanol (or appropriate solvent)
4. Calibrated micropipettes
5. Container for mixing thiol solution (solution container)
6. Tweezers for sample handling
7. A dedicated ethanol solvent bottle
8. Parafilm for sealing containers
9. Containers for sample preparation (sample containers)
10. Petri dishes for transporting and storing SAMs
11. Dry nitrogen
12. Analytical Balance
13. Sonicator
14. pH paper
Environment: A clean environment is key to preparing quality
SAMs. Low levels of contaminants can affect monolayer
quality. Avoid rooms or hoods in which silanes or poly(dimethyl
siloxane) (PDMS) have been used. These compounds easily cross
contaminate a variety of surfaces. Iodine adsorbs readily onto
gold and should be avoided.
Handle all thiols in a fume hood. Most thiols have an obnoxious
odor and are toxic (check MSDS before using).
Containers: Appropriate containers include glass or
polypropylene (e.g., scintillation vials, polypropylene test
tubes and centrifuge tubes). Glass containers must be cleaned
thoroughly to avoid solution contamination.
Containers that can be easily sealed are recommended. For the
highest quality films, oxygen exposure should be minimized
during the assembly process. This is achieved by reducing the
headspace above the thiol solution and backfilling with an
inert gas. Each substrate is placed in its own container to avoid
interactions that would be detrimental to film quality.
1
One option for glass cleaning is the use of piranha solution (30:70 v/v
solution of 30% hydrogen peroxide (H2O2) and concentrated sulfuric acid
(H2SO4)). Extreme caution has to be taken when using piranha solution.
It is a very strong oxidant and reacts violently with organic matter.
s i g m a - a l d r i c h . c o m
Containers can be reused, as long as they are rinsed well with
solvent after each use and dedicated to the same thiol to avoid
cross-contamination.
TO ORDER: Contact your local Sigma-Aldrich office (see back cover),
call 1-800-325-3010 (USA), or visit sigma-aldrich.com/matsci.
Solvent: For most thiols, pure ethanol (200 proof) is required
for successful assembly. Alternately, denatured alcohol,
containing up to 5% isopropanol and/or methanol, is a
suitable substitute. Solvent purity should be verified due
to potential contamination by copper. Copper disrupts the
assembly of the thiols and may affect the performance of the
resulting SAM.
Sample Slides: Gold slides must have an adhesion layer of
chromium (Cr) or titanium (Ti) under the gold layer. If this layer
is missing the gold will delaminate and ruin the monolayer
during sonication.
Dedicated wash bottle: It is best to have a dedicated solvent
wash bottle used for rinsing containers, substrates and SAMs.
Store the bottle empty and only fill it with fresh ethanol when
needed.
Step-by-Step Procedure
This general protocol is appropriate for most thiols. Thiols
containing amine, carboxy groups require modifications to
the protocol as noted in green below. The properties of PEG
thiol monolayers depend on the method of self-assembly.
Researchers should review references 5–7 before using these
materials.
1. Determine necessary amounts and concentration of
thiol solution.
a. Calculate the total volume of thiol solution needed to make
the number of samples desired.
[Total volume of solution (mL)] = [total number of samples] x
[Sample solution volume (mL)]
b. C
 alculate the total amount of thiol needed to prepare
desired amount of solution. (where C = 1-5 mM solutions)
[Mass of thiol (g)] = [Total Volume (mL)] x [C x 10-6 mol/ml] x
[MW(g/mol)]
If the thiol is a liquid, you can convert the mass to a volume
using the density of the thiol. Use a calibrated micropipette for
measuring and dispensing liquid thiols.
2. Preparing the thiol solution. Prepare enough solution for
all samples to ensure the solution concentration is constant
across the sample set. When preparing mixed thiol solutions,
prepare a stock solution of each thiol separately, then mix
them at the proper proportions for the final stock solution.
a. R
 inse all assembly containers with solvent by squirting ~3 to
5 mL around the inside of the containers. Repeat 2–3 times
and re-cap each container. Rinse all beakers, tweezers,
etc., to be used in the experiment with solvent. Label all
containers.
b. M
 easure the appropriate volume of solvent into the clean
solution container.
c. Dispense the mass (or volume) of thiol, to the solvent.
d. Sonicate the container 5–10 min to dissolve.
e. Once dissolved, dispense the planned volume of solution
into each sample container.
 US $ 19

•C
 arboxy terminated thiols: Adjust the solution pH to ~2 200 Proof Ethanol 
with a few drops of concentrated HCl. Then sonicate stock Sigma-Aldrich simplifies your purchase of 200-proof ethanol
solution. by immediately filing ATF paperwork and paying the federal
•A
 mine terminated thiols: Adjust the solution pH to ~12 with excise tax for you!
concentrated NH4Cl or triethylamine. Then sonicate stock
solution. 459844-1 L ACS reagent, ≥99.5%
459836-1 L Anhydrous, ≥99.5%
3. Sample Self-Assembly.
459828-1 L HPLC/spectrophotometric grade
a. Immerse gold substrate in container containing the thiol
solution. Handle gold substrates with tweezers and E7023-500 mL Absolute for molecular biology 
minimize expose to air, to reduce surface contaminants. 493546-500 mL USP/NF
b. B
 ackfill each container with dry nitrogen and seal the cap For a complete list of our Tax-Paid Ethanol’s, please visit us at
sigma-aldrich.com/solvents and select High-Purity dropdown.
and wrap the cap with Parafilm.
c. S tore the sample for at least 24 to 48 hours. In general,
Labware for SAMs

Preparation
Protocol for SAMs
longer assembly times tend to result in better packing of the
monolayers. Find these Labware products
on our Web site at
4. T
 erminating self-assembly: Functional groups on the sigma-aldrich.com/labware
thiols affect self-assembly termination.
keyword search:
For simple alkanethiols: microcapillary pipettes,
a. H
 old the sample with clean tweezers and rinse with solvent tweezers, sigma-aldrich wash,
for 10 to 15 seconds from a clean solvent bottle. bottles (ethanol), parafilm,
scintillation vials or test
b. Dry sample with a stream of dry nitrogen.
tubes, petri dishes, analytical
For thiols with hydrogen-bonding, polar or bulky head groups: balances, sonicator, pH paper
c. H
 old the sample with clean tweezers and rinse with solvent Ultrasonic Cleaner
for 10 to 15 seconds from a clean solvent bottle. (Solvent
should be pH adjusted for carboxy and amine terminated
SAMs)
d. P lace each sample in a container with fresh solvent and Coming Soon!
close the cap. (Again solvent should be pH adjusted if The NEW 2007–2008
needed)
Aldrich Handbook of Fine Chemicals
e. Sonicate the samples for 1–3 minutes.
Includes a Materials Science Application Index with
f. R
 emove the samples individually and rinse again for 10–15 products organized in application

O r d e r :
seconds under a steady stream of ethanol. (At this stage no
groups for easy reference
pH adjustment is necessary. Use pure solvent)
and browsing.
g. Dry sample with a stream of dry nitrogen.

1 . 8 0 0 . 3 2 5 . 3 0 1 0
5. Sample Storage
a. Place in clean Petri dish.
b. Backfill Petri dish with dry nitrogen.
c. F or long-term storage: Place the Petri dishes in a jar
backfilled with dry N2 and sealed with Parafilm.
Topics
If you are going to use the monolayers for further • Chemical Solution Deposition/Sol-Gel Processing
experimentation, plan your experiments so you can rinse the • Chemical Vapor Deposition
samples right before use. Minimize time between preparation • Conducting Polymers
Te c h n i c a l

and use since SAMs can oxidize over time. • Fuel Cells
References
- Materials for Hydrogen Storage
(1) Love, C.; Estroff, L.; Kriebel, J.; Nuzzo, R.; Whitesides, G.; Chem. Rev., - Proton Exchange Membrane (PEM) Materials
2005, 105, 1103–1170. (2) Arnold, R.; Azzam, W.; Terfort, A.; Woll, C., • Nanoparticles
Langmuir, 2002, 18, 3980–3992. (3) Wang, H.; Chen, S. F.; Li, L. Y.; Jiang, - Nanopowders & Nanodispersions
S. Y., Langmuir, 2005, 21, 2633–2636. (4) Noh, J.; Konno, K.; Ito, E.; Hara, - Functionalized Nanoparticles
S e r v i c e :

M., Jpn. J. Appl. Phys. Part 1 2005, 44, 1052–1054. (5) Li, L. Y.; Chen, - Quantum Dots
S. F.; Zheng, J.; Ratner, B. D.; Jiang, S. Y., J. Phys. Chem. B 2005, 109, • Electronic Grade Materials
2934–2941. (6) Herrwerth, S.; Eck, W.; Reinhardt, S.; Grunze, M., J. Am.
Chem. Soc. 2003, 125, 9359–9366. (7) Harder, P.; Grunze, M.; Dahint, R.; Reserve Your Free Copy of the
Whitesides, G. M.; Laibinis, P. E., J. Phys. Chem. B 1998, 102, 426–436 Aldrich Handbook Today!
sigma-aldrich.com/handbook2
1 . 8 0 0 . 2 3 1 . 8 3 2 7

For questions, product data, or new product suggestions,

please contact the Materials Science team at matsci@sial.com.
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